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Honestly the alignment never crossed my mind until you said something.. It looks like this is actually a common issue on the Chevy blocks, and offset dowel pins are available.. Found this site which shows quite a bit of info
CRG Research Report - Bellhousing Alignment
Like Dave pointed out, it is critical that the tranny bearing retainer be a snug fit in the bellhousing center hole. The four bolts on the tranny to bellhousing do nothing but pull everything together and hold it there. They provide zero alignment function. You need to bolt your bellhousing on the engine, then using a dial indicator with magnetic base attached to the flywheel, check the alignment of the bellhousing center hole to the crankshaft. Anything over 0.005 needs to be corrected with alignment dowels to ensure that the bellhousing is straight with the crank. Once that's done, the alignment of the tranny is done. Slide the tranny into place with the input bearing retainer snug in the bellhousing, and check your four tranny retaining bolt holes for alignment. Once you have the three that are close figured out, mark the fourth one and send your bellhousing to Severson to fix.
Or, buy a chevy tranny and make your life less stressful.